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- PDB-3mon: CRYSTAL STRUCTURES OF TWO INTENSELY SWEET PROTEINS -

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Basic information

Entry
Database: PDB / ID: 3mon
TitleCRYSTAL STRUCTURES OF TWO INTENSELY SWEET PROTEINS
Components(MONELLIN) x 2
KeywordsSWEET-TASTING PROTEIN
Function / homology
Function and homology information


Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular ...Helix Hairpins - #2000 / N-terminal domain of TfIIb - #130 / Monellin, A chain / Monellin, A chain superfamily / Monellin, B chain / Monellin / Monellin / N-terminal domain of TfIIb / Cystatin superfamily / Other non-globular / Helix Hairpins / Helix non-globular / Special
Similarity search - Domain/homology
Monellin chain A / Monellin chain B
Similarity search - Component
Biological speciesDioscoreophyllum cumminsii (serendipity berry)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsJiang, F. / Tong, L. / Kim, S.-H.
Citation
Journal: Trends Biochem.Sci. / Year: 1988
Title: Crystal structures of two intensely sweet proteins.
Authors: Kim, S.H. / de Vos, A. / Ogata, C.
#1: Journal: Nature / Year: 1987
Title: Crystal Structure of the Intensely Sweet Protein Monellin
Authors: Ogata, C. / Hatada, M. / Tomlinson, G. / Shin, W.-C. / Kim, S.-H.
#2: Journal: Biochemistry / Year: 1983
Title: Crystal Structure of a Sweet Protein, Monellin, at 5.5-Angstroms Resolution
Authors: Tomlinson, G. / Ogata, C. / Shin, W.-C. / Kim, S.-H.
#3: Journal: J.Biol.Chem. / Year: 1981
Title: Preliminary Crystallographic Studies of a Sweet Protein, Monellin
Authors: Tomlinson, G. / Kim, S.-H.
History
DepositionAug 26, 1992Processing site: BNL
SupersessionOct 15, 1993ID: 1MON
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Remark 700SHEET EACH MOLECULE CONTAINS A SHEET CONSISTING OF STRANDS FROM BOTH CHAINS. ONE OF THE STRANDS ...SHEET EACH MOLECULE CONTAINS A SHEET CONSISTING OF STRANDS FROM BOTH CHAINS. ONE OF THE STRANDS CONTAINS A BULGE AND THIS IS REPRESENTED BY PRESENTING THE SHEET TWICE EACH WITH PART OF THAT STRAND.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MONELLIN
B: MONELLIN
C: MONELLIN
D: MONELLIN
E: MONELLIN
F: MONELLIN
G: MONELLIN
H: MONELLIN


Theoretical massNumber of molelcules
Total (without water)44,4078
Polymers44,4078
Non-polymers00
Water0
1
A: MONELLIN
B: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-21 kcal/mol
Surface area6020 Å2
MethodPISA
2
C: MONELLIN
D: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2460 Å2
ΔGint-20 kcal/mol
Surface area6080 Å2
MethodPISA
3
E: MONELLIN
F: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area6070 Å2
MethodPISA
4
G: MONELLIN
H: MONELLIN


Theoretical massNumber of molelcules
Total (without water)11,1022
Polymers11,1022
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-20 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.840, 87.200, 72.060
Angle α, β, γ (deg.)90.00, 90.00, 107.30
Int Tables number4
Space group name H-MP1121
Atom site foot note1: CIS PROLINE - PRO A 41 / 2: CIS PROLINE - PRO B 40 / 3: CIS PROLINE - PRO C 41 / 4: CIS PROLINE - PRO D 40 / 5: CIS PROLINE - PRO E 41 / 6: CIS PROLINE - PRO F 40 / 7: CIS PROLINE - PRO G 41 / 8: CIS PROLINE - PRO H 40

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Components

#1: Protein/peptide
MONELLIN /


Mass: 5259.993 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02881
#2: Protein/peptide
MONELLIN /


Mass: 5841.647 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dioscoreophyllum cumminsii (serendipity berry)
References: UniProt: P02882
Sequence detailsSEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: ...SEQUENCE ADVISORY NOTICE: DIFFERENCE BETWEEN SWISS-PROT AND PDB SEQUENCE. SWISS-PROT ENTRY NAME: MONB_DIOCU MONELLIN SWISS-PROT RESIDUE PDB SEQRES NAME NUMBER NAME CHAIN SEQ/INSERT CODE GLU 49 ASN B 49 ASN 50 GLU B 50 GLU 49 ASN D 49 ASN 50 GLU D 50 GLU 49 ASN F 49 ASN 50 GLU F 50 GLU 49 ASN H 49 ASN 50 GLU H 50

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14 mg/mlprotein 1drop
210 mMphosphate1drop
333.3 %(w/w)PEG60001reservoir

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Processing

SoftwareName: X-PLOR / Classification: refinement
RefinementRfactor Rwork: 0.193 / Highest resolution: 2.8 Å
Details: PLEASE NOTE THAT THE SPACE GROUP GROUP SETTING USED IN THIS ENTRY IS THE FIRST SETTING (Z-AXIS UNIQUE).
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3136 0 0 0 3136

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